Merge branch '1.0.x' into 'master'

CHANGELOG.md

@@ -11,14 +11,19 @@ Features:
 * Configuration file contains the walltime taken by each run
 * It is now possible to upload or download any file via its full path
 
-1.0.16 (???)
-------------
+1.0.16 (2019-02-06)
+-------------------
+
+(reprozip-jupyter and reprounzip-vagrant didn't change)
 
 Bugfixes:
 * Fixed input/output file filter on Python 3 (to omit `.so`, `.pyc` etc files)
+* Fixed fetching updated parameters on Python 3 (to get the correct Docker and Vagrant base images, a small JSON file is downloaded from reprozip.org)
+* Fixed `--port` option of reprounzip-docker
 
 Enhancements:
 * Use the [distro](https://distro.readthedocs.io/) module instead of the deprecated `platform.linux_distribution()` function to detect the distribution (the latter will be removed in Python 3.8).
+* Use dpkg-query to identify Linux packages instead of reading `dpkg/info/*.list`
 
 1.0.15 (2018-07-31)
 -------------------

README.md

@@ -1,10 +1,10 @@
-[![Build Status](https://travis-ci.org/ViDA-NYU/reprozip.svg?branch=master)](https://travis-ci.org/ViDA-NYU/reprozip)
-[![Coverage Status](https://codecov.io/github/ViDA-NYU/reprozip/coverage.svg?branch=master)](https://codecov.io/github/ViDA-NYU/reprozip?branch=master)
+[![Build Status](https://travis-ci.org/VIDA-NYU/reprozip.svg?branch=master)](https://travis-ci.org/VIDA-NYU/reprozip)
+[![Coverage Status](https://codecov.io/github/VIDA-NYU/reprozip/coverage.svg?branch=master)](https://codecov.io/github/VIDA-NYU/reprozip?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/reprozip/badge/?version=latest)](https://docs.reprozip.org/en/latest/)
 [![Matrix](https://img.shields.io/badge/chat-matrix.org-blue.svg)](https://riot.im/app/#/room/#reprozip:matrix.org)
 [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/remram44)
 [![status](https://img.shields.io/badge/JOSS-10.21105%2Fjoss.00107-green.svg)](http://joss.theoj.org/papers/b578b171263c73f64dfb9d040ca80fe0)
-[![DOI](https://img.shields.io/badge/DOI/10.5281%2Fzenodo.1324502-green.svg)](https://doi.org/10.5281/zenodo.1324502)
+[![DOI](https://img.shields.io/badge/DOI/10.5281%2Fzenodo.2558333-green.svg)](https://doi.org/10.5281/zenodo.2558333
 
 ReproZip
 ========
@@ -16,7 +16,7 @@ It tracks operating system calls and creates a package that contains all the bin
 Quickstart
 ----------
 
-We have an [example repository](https://github.com/ViDA-NYU/reprozip-examples) with a variety of different software. Don't hesitate to check it out, and contribute your own example if use ReproZip for something new!
+We have an [example repository](https://github.com/VIDA-NYU/reprozip-examples) with a variety of different software. Don't hesitate to check it out, and contribute your own example if use ReproZip for something new!
 
 ### Packing
 
@@ -103,9 +103,9 @@ Please subscribe to and contact the [reprozip-users](https://vgc.poly.edu/mailma
 
 Use the [reprozip-dev](https://vgc.poly.edu/mailman/listinfo/reprozip-dev) mailing list for any questions about reprozip source code.
 
-Bugs and feature plannings are tracked in the [GitHub issues](https://github.com/ViDA-NYU/reprozip/issues). Feel free to add an issue!
+Bugs and feature plannings are tracked in the [GitHub issues](https://github.com/VIDA-NYU/reprozip/issues). Feel free to add an issue!
 
-To suggest changes to this source code, feel free to raise a [GitHub pull request](https://github.com/ViDA-NYU/reprozip/pulls).  Any contributions received are assumed to be covered by the [BSD 3-Clause license](LICENSE.txt). We might ask you to sign a _Contributor License Agreement_ before accepting a larger contribution.
+To suggest changes to this source code, feel free to raise a [GitHub pull request](https://github.com/VIDA-NYU/reprozip/pulls).  Any contributions received are assumed to be covered by the [BSD 3-Clause license](LICENSE.txt). We might ask you to sign a _Contributor License Agreement_ before accepting a larger contribution.
 
 License
 -------

docs/gui.rst

@@ -14,7 +14,7 @@ If you are using Anaconda, you can install *reprounzip-qt* from anaconda.org::
 
     $ conda install --channel vida-nyu reprounzip-qt
 
-Otherwise, you will need to `install PyQt4 <https://www.riverbankcomputing.com/software/pyqt/download>`__ before you can install *reprounzip-qt* from pip (on Debian or Ubuntu, you can use ``apt-get install python-qt4``).
+Otherwise, you will need to `install PyQt4 <https://www.riverbankcomputing.com/software/pyqt/download>`__ (or `PyQt5 <https://www.riverbankcomputing.com/software/pyqt/download5>`__) before you can install *reprounzip-qt* from pip (on Debian or Ubuntu, you can use ``apt-get install python-qt4``).
 
 Usage
 =====

docs/install.rst

@@ -193,7 +193,7 @@ Or you can install *reprounzip* and choose components manually::
 Anaconda
 ========
 
-*reprozip* and *reprounzip* can also be installed on the `Anaconda <https://www.anaconda.com/download/>`__ Python distribution, from anaconda.org::
+*reprozip* and *reprounzip* can also be installed on the `Anaconda <https://www.anaconda.com/distribution/>`__ Python distribution, from anaconda.org::
 
     $ conda install --channel vida-nyu reprozip reprounzip reprounzip-docker reprounzip-vagrant reprounzip-vistrails
 

reprounzip-qt/reprounzip_qt/__init__.py

@@ -1 +1 @@
-__version__ = '1.0.15'
+__version__ = '1.0.16'

reprounzip-qt/reprounzip_qt/gui/__init__.py

@@ -6,7 +6,7 @@
 
 import logging
 import os
-from PyQt4 import QtCore, QtGui
+from qtpy import QtCore, QtWidgets
 import shutil
 import subprocess
 import sys
@@ -24,9 +24,9 @@
 logger = logging.getLogger('reprounzip_qt')
 
 
-class Application(QtGui.QApplication):
+class Application(QtWidgets.QApplication):
     def __init__(self, argv):
-        QtGui.QApplication.__init__(self, argv)
+        QtWidgets.QApplication.__init__(self, argv)
         self.first_window = None
         self.windows = set()
 
@@ -48,14 +48,14 @@ def linux_try_register_default(self, window):
             logger.info("xdg-mime call failed, not registering application")
         else:
             if not registered:
-                r = QtGui.QMessageBox.question(
+                r = QtWidgets.QMessageBox.question(
                     window, "Default application",
                     "Do you want to set ReproUnzip as the default to open "
                     ".rpz files?",
-                    QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
-                if r == QtGui.QMessageBox.Yes:
+                    QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No)
+                if r == QtWidgets.QMessageBox.Yes:
                     self.linux_register_default(window)
-                elif r == QtGui.QMessageBox.No:
+                elif r == QtWidgets.QMessageBox.No:
                     record_usage(appregister='no')
                     if not os.path.exists(rcpath):
                         os.mkdir(rcpath)
@@ -127,22 +127,22 @@ def linux_register_default(self, window):
             shutil.rmtree(dirname)
 
     def ask_enable_usage_report(self):
-        dialog = QtGui.QDialog()
+        dialog = QtWidgets.QDialog()
         dialog.setWindowTitle("Anonymous usage statistics")
-        layout = QtGui.QVBoxLayout()
-        layout.addWidget(QtGui.QLabel("Send anonymous usage reports to the "
-                                      "developers?"))
-        dont_ask = QtGui.QCheckBox("Don't ask again")
+        layout = QtWidgets.QVBoxLayout()
+        layout.addWidget(QtWidgets.QLabel("Send anonymous usage reports to "
+                                          "the developers?"))
+        dont_ask = QtWidgets.QCheckBox("Don't ask again")
         layout.addWidget(dont_ask)
-        buttons = QtGui.QDialogButtonBox(
-            QtGui.QDialogButtonBox.Yes | QtGui.QDialogButtonBox.No)
+        buttons = QtWidgets.QDialogButtonBox(
+            QtWidgets.QDialogButtonBox.Yes | QtWidgets.QDialogButtonBox.No)
         layout.addWidget(buttons)
         buttons.accepted.connect(dialog.accept)
         buttons.rejected.connect(dialog.reject)
         dialog.setLayout(layout)
 
         res = dialog.exec_()
-        if res == QtGui.QDialog.Accepted:
+        if res == QtWidgets.QDialog.Accepted:
             usage_report.enable_reporting()
         elif dont_ask.isChecked():
             usage_report.disable_reporting()
@@ -160,7 +160,7 @@ def event(self, event):
                 self.first_window.deleteLater()
                 self.first_window = None
             return True
-        return QtGui.QApplication.event(self, event)
+        return QtWidgets.QApplication.event(self, event)
 
     def set_first_window(self, window):
         self.first_window = window
@@ -171,11 +171,13 @@ def set_first_window(self, window):
             self.ask_enable_usage_report()
 
 
-class ReprounzipUi(QtGui.QMainWindow):
+class ReprounzipUi(QtWidgets.QMainWindow):
     def __init__(self, unpack={}, run={}, tab=None, **kwargs):
         super(ReprounzipUi, self).__init__(**kwargs)
 
-        self.tabs = QtGui.QTabWidget()
+        self.setWindowTitle("ReproUnzip")
+
+        self.tabs = QtWidgets.QTabWidget()
         self.tabs.addTab(UnpackTab(**unpack), "Open package")
         self.tabs.addTab(RunTab(**run), "Run unpacked experiment")
         self.tabs.widget(0).unpacked.connect(self._unpacked)

reprounzip-qt/reprounzip_qt/gui/common.py

@@ -4,21 +4,22 @@
 
 from __future__ import division, print_function, unicode_literals
 
-from PyQt4 import QtCore, QtGui
+from qtpy import QtCore, QtWidgets
 import re
 
 
 def error_msg(parent, message, severity, details=None):
     if severity == 'information':
-        icon = QtGui.QMessageBox.Information
+        icon = QtWidgets.QMessageBox.Information
     elif severity == 'warning':
-        icon = QtGui.QMessageBox.Warning
+        icon = QtWidgets.QMessageBox.Warning
     else:
-        icon = QtGui.QMessageBox.Critical
+        icon = QtWidgets.QMessageBox.Critical
 
-    msgbox = QtGui.QMessageBox(icon, "Error", message, QtGui.QMessageBox.Ok,
-                               parent, detailedText=details,
-                               textFormat=QtCore.Qt.PlainText)
+    msgbox = QtWidgets.QMessageBox(icon, "Error", message,
+                                   QtWidgets.QMessageBox.Ok, parent,
+                                   detailedText=details,
+                                   textFormat=QtCore.Qt.PlainText)
     msgbox.exec_()
 
 
@@ -30,22 +31,22 @@ def handle_error(parent, result):
         return False
 
 
-class ResizableStack(QtGui.QStackedWidget):
+class ResizableStack(QtWidgets.QStackedWidget):
     # See http://stackoverflow.com/a/14485901/711380
     def __init__(self, **kwargs):
         super(ResizableStack, self).__init__(**kwargs)
 
         self.currentChanged[int].connect(self._current_changed)
 
     def addWidget(self, widget):
-        widget.setSizePolicy(QtGui.QSizePolicy.Ignored,
-                             QtGui.QSizePolicy.Ignored)
+        widget.setSizePolicy(QtWidgets.QSizePolicy.Ignored,
+                             QtWidgets.QSizePolicy.Ignored)
         super(ResizableStack, self).addWidget(widget)
 
     def _current_changed(self, idx):
         widget = self.widget(idx)
-        widget.setSizePolicy(QtGui.QSizePolicy.Expanding,
-                             QtGui.QSizePolicy.Expanding)
+        widget.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
+                             QtWidgets.QSizePolicy.Expanding)
         widget.adjustSize()
         self.adjustSize()